chr2-44478476-A-G

Position:

• chr2-44478476-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024766.5(CAMKMT):​c.376+88171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 151,872 control chromosomes in the GnomAD database, including 49,811 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (49811 hom., cov: 31)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

CAMKMT (HGNC:26276): (calmodulin-lysine N-methyltransferase) This gene encodes a class I protein methyltransferase that acts in the formation of trimethyllysine in calmodulin. The protein contains a AdoMet-binding motif and may play a role in calcium-dependent signaling. [provided by RefSeq, Sep 2012]

LOC124907758 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+88171A>G		intron_variant		ENST00000378494.8	NP_079042.1
LOC124907758	XR_007086302.1	n.2686A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+88171A>G		intron_variant		1	NM_024766.5	ENSP00000367755	P1
CAMKMT	ENST00000402247.5	c.377-71079A>G		intron_variant		2		ENSP00000385587
CAMKMT	ENST00000407131.5	c.376+88171A>G		intron_variant		3		ENSP00000384039
CAMKMT	ENST00000428993.1	c.207-71079A>G		intron_variant, NMD_transcript_variant		3		ENSP00000410783

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122345 AN: 151754 Hom.: 49745 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.814

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.806 AC: 122472 AN: 151872 Hom.: 49811 Cov.: 31 AF XY: 0.802 AC XY: 59538 AN XY: 74196

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.815

Alfa AF: 0.775 Hom.: 42455

Bravo AF: 0.821

Asia WGS AF: 0.789 AC: 2741 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	13
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs698813; hg19: chr2-44705615;